


Section 31

by WillSherJohnKhan



Category: Sherlock (TV), Star Trek: Into Darkness - Fandom
Genre: AU, Betrayal, F/M, False data trails, Fighting for Survival, Help from an unexpected quarter, Khan's fury unleashed, Misdirection, Searching for answers, who to trust
Language: English
Status: In-Progress
Published: 2016-03-07
Updated: 2017-11-23
Packaged: 2018-05-25 06:31:03
Rating: Mature
Warnings: Graphic Depictions Of Violence
Chapters: 3
Words: 3,338
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/6184327
Author URL: https://archiveofourown.org/users/WillSherJohnKhan/pseuds/WillSherJohnKhan
Summary: <blockquote class="userstuff">
              <p>It is said that ‘Power corrupts, and absolute power corrupts absolutely.’<br/>Or to put it another way: ‘Welcome to Section 31’</p><p>This story is a follow up to A Phoenix Rises.</p><p>Disclaimer:<br/>I don’t own any of these characters. I just like to play with them every now and then.</p>
            </blockquote>





	1. Prologue

***

Those that had volunteered for the mission did so knowing they were going up against a formidable opponent.

Section 31 was never officially acknowledged, but its dominant and imposing presence was felt throughout Starfleet and the Federation.

To go after such an organization and its agents was regarded by many as reckless, if not downright suicidal. 

*

Fear had led to Section 31’s creation, and they used that fear as justification for the questionable methods they employed. Their operations were kept hidden behind a veil of secrecy that they deemed as necessary if they were to effectively protect the Federation and its citizens. 

Therefore, Section 31 was accountable to no one. They existed outside Starfleet and the Federation’s influence. This meant they were not subject to the constraints of Starfleet’s ethical protocols. In their arrogance they saw themselves as the ultimate intelligence and security agency. And as such, they saw no need to submit reports about their activities to anyone, or to request permission for the undertaking of their operations. Their credo that to save lives, ‘the ends always justified the means’ meant that their interrogation techniques routinely included the brainwashing and torturing of suspects, some of who were the very citizens they claimed to protect. To enhance their ability to defend planetary systems in the Federation from possible attack, they had developed advanced weaponry and constructed warships. Assassinations and the committing of genocide were justified as an absolute imperative in the interests of inter-galactic security from potential external threats.

So when the true nature of their activities did eventually come to light and the lengths they were prepared to go were revealed, it shocked and sickened many. It was clear that Section 31 was a loose cannon, and posed far more of a threat to the security of the Federation than any potential exterior influence.

But many in Starfleet Command and the Federation’s Governing Council were too afraid to mount a move against them. The hold Section 31 had over them was still too strong. Instead they turned a blind eye and allowed them to make their escape.

*

Starfleet refused to sanction the mission. They made their position very clear on that point. If those who chose to take part in such a risky assignment, then they did so in the full knowledge that they were on their own. They weren’t to use anything that could identify them as being part of Starfleet.

But if Starfleet Command believed these restrictions would make the group rethink their position, then they were to be disappointed.

It only reinforced their determination.

It may have made getting what they needed to undertake their mission that more difficult, but not impossible. 

It was essential that they had a ship, which was their top priority. Since the Enterprise was now out of the question, their thoughts turned to another… A stealth ship with advanced weaponry. Its inclusion would be vital if their mission was to have any chance of success.

Unfortunately it was currently stored, in its badly damaged condition at a junkyard outside San Francisco.

In secret they had the ship moved to the very shipyard formally controlled by Section 31 that had been abandoned immediately after the death of Alexander Marcus.

It was here, far away from prying eyes, that the rebuilding of the dreadnaught-class warship began.

***

IO FACILITY, NEAR THE JUPITOR MOON - THREE MONTHS LATER

Disengaging from the shipyards docking port, the Vengeance manoeuvred free of its moorings and slipped noiselessly back into the outer reaches of deep space.

*

VENGEANCE – BRIDGE

Seated in the Captain’s chair, James T. Kirk observed his fellow volunteers. Like him they were ready and eager to begin their mission.

His gaze settled on Khan, if he felt any anxiety or inner turmoil he didn’t show it. Outwardly he gave the impression of complete calm, whatever his true feelings they remained hidden, which was a testament to his strength of character, given he had the most to gain, or lose, depending on the outcome of the mission.

Turning back to his helmsman Kirk gave the order. “All right Mr Sulu, go to warp.”

The time had finally come for the implementing of their self-appointed assignment: that of the tracking down Section 31, and discovering the whereabouts of the missing 72 augments.

***


	2. Welcome Back

**Summary for the Chapter:**

> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

**Notes for the Chapter:**

> For anyone who has read the graphic novel Star Trek: Khan, much about this chapter will be familiar, although I have made certain alterations. I enjoyed the story it told very much, though a little light on detail. So my intention here, and with other flashbacks is to flesh the story out a bit. :-)

***

IO FACILITY – 2258.15

“John? John can you hear me?” a disembodied voice worked its way into his consciousness. With a struggle he fought his way through what felt like an impenetrable fog in his mind, eventually winning the battle as his eyes flickered open, though his eyelids still felt so heavy, he found it difficult to focus of the face that belonged to the voice.

“That’s it John,” Admiral Marcus continued encouragingly as the man lying on the bio-bed finally regained consciousness. “Welcome back.”

The man named John looked blearily at the man leaning over him. He opened his mouth to speak, but his mouth was so dry, he had to swallow several times to generate enough saliva, so he could wet his parched lips with his tongue. Turning his head to try and assess where he was exactly left him feeling dizzy and confused. “Wh… Where…?” he began uncertainly.

“Your eyes should adjust to the light in no time,” the man assured him.

“… Am I...?”

“Home, John. You’ve come home.”

“Home,” he repeated. His eyelids, that felt like they weighed a tonne, began to close again.

Marcus went to the replicator before returning to the bed to press a glass of water to John’s lips. “Here,” he said as he placed a supporting hand to the man’s upper back and neck. “This might help.”

John greedily swallowed down the fresh, cool contents of the glass.

“Better?” the admiral asked.

“Much,” John replied gratefully, leaning back with an exhausted sigh, his gaze however remained focussed on the other man.

Marcus read the unasked question in ‘John’s’ eyes. Seeing little point in delaying matters, the admiral set into motion the next stage of the plan he’d devised, upon discovering the true identity of the man now lying in the bed before him.

“You probably wont remember much of this, or anything for that matter,” he advised. “But my name is Alex Marcus, and we’ve been friends for years.”

“Alex… And I’m… I’m John,” John responded cautiously.

“That’s right,” Marcus confirmed encouragingly. “You’re a Starfleet officer, Commander John Harrison…”

John frowned. Mention of Starfleet triggered a brief flash of memory. But the rank Alex had given him, it didn’t feel… right.

Marcus cut into his thoughts. “Sorry, getting a little ahead of myself. At the time of your mission to QoNo’s, the Klingon Homeworld, you were a Lieutenant. You have since been promoted to Commander.”

“Klingon… QoNo’s…” John murmured thoughtfully.

“Yes. Six months ago you were critically injured while on a mission to the Klingon’s Homeworld. You suffered brain trauma that should have left you catatonic for life,” Marcus explained. “But the best surgeons in Starfleet, and the fact you’re the toughest bastard I know brought you back.”

Although Alex sounded enthusiastic, John was starting to feel somewhat overwhelmed. He tried desperately to remember the events Marcus spoke of. But, try as he might, he came up blank.

“I don’t remember,” he exclaimed, his voice rising as panic threatened to engulf him. “I don’t know who I am… what I do… Starfleet…?”

As Marcus observed the man before him, he inwardly gloried at seeing this man, who had at one time ruled more than a quarter of the Earth’s population, reduced to his current state of hysteria. But outwardly he moved to reassure the agitated man, placing a calm but restraining hand on his shoulder, pressing him gently back to a reclining position. “Its all right John, you will remember, it will just take a little time. But don’t worry I’m going to help you. The more you re-learn, the more you’ll remember on your own. Its early days, and they’ll prove the hardest. But I promise you, you wont go through them alone.”

He felt the tension in John’s body ease, and his breathing calmed. “I’ll leave you now to get some sleep. The doctors warned me I shouldn’t get you over-excited.”

When John’s eyes closed the admiral took his leave, satisfied that the latest stage of his plan had gone off without a hitch. But he knew he needed to be cautious, Khan Noonien Singh was not the type of man who would take kindly to being manipulated.

***


	3. Evil at Heart

**Summary for the Chapter:**

> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

***

MISSION DAY 21

VENGEANCE – TRANSPORTER SECTION

As Captain James T. Kirk made his way to the transporter pad, he occupied his mind with marvelling at the simplicity of the warship they now travelled on. Where the Enterprise had been all about a comfortable environment for a life of exploring the wide and uncharted universe, the Vengeance was about stripping comforts and everything else down to the bare minimum. Hence an actual room for the transporters was regarded as unnecessary, so a section just off Medical had been set aside for the placement of the transporter pads and terminal.

Whispers and rumours were all that they had to go on. Such was the nature of their task in tracking down Section 31’s movements. That was the damned annoying situation they found themselves with in their self-appointed mission. It was for this reason that he was eager to hear what, if anything the away team had learned after their survey of the planet below.

Communication between the ship and the away team had been intermittent from the moment they had transported down to the surface of what was believed to be an uninhabited planet, Vagra II.

*

When the three crew members rematerialised, Kirk was relieved to note that all three appeared unharmed, though it was clear that Khan had survived an interesting encounter.

The once legendary former-leader, clandestine operative, accused traitor and now valued crew member looked the worse for wear. The augments usual immaculate self now covered from head to toe in a sticky black, oozing goo. And it was clear from his annoyed expression that he was not happy about it.

Kirk couldn’t help teasing his newly appointed Head of Security, querying cheerfully. “Negotiations go well then?” 

Khan spared his Captain a brief irritated glare, muttering under his breath as he stalked off. “It got the message.”

Kirk raised an enquiring eyebrow at Spock and Bones. “I look forward to reading your reports.”

***

VAGRA II – EARLIER

From the moment Mr Spock, Dr McCoy and Khan arrived on the surface of the desolate planet they all had the uncomfortable feeling that they were being watched.

This was completely at odds with the data on their tri-corders, not to mention the Vengeance’s far superior scanners that all showed Vagra II to be devoid of sentient life.

And yet the feeling persisted.

From where they stood all they could see was a dry, lifeless landscape made up of rock and sand. The sky above them had a sickly orange hue to it that was continually highlighted by violent electrical storms.

The only other feature of interest was an area of ground that appeared to be covered in a tar-like sludge.

Though there seemed to be little prospect of finding any clues as to why Section 31 would have come here, they nonetheless set about searching the surrounding area to assure themselves that there was nothing here to find.

They were just finishing their reconnaissance and were back at the point from where they had started, when McCoy looked about him, a frown forming as he tried to work something out.

“Problem doctor,” Spock queried.

“Yeah,” McCoy responded. “When we were here before, wasn’t that black stuff further over that way?”

Khan and Spock checked the readings on their tri-corders and found that the doctor was quite correct.

Khan took a step towards the unknown substance intending to get a clearer reading of it, when...

“Look out!” came McCoy’s warning shout, but too late.

The puddle moved swiftly to completely engulf the unwary augment.

As Khan disappeared from view, a menacing voice cackled. “You’ll do nicely.”

*

Khan fought to free himself, but to no avail. It was only when he sensed the enjoyment and immense satisfaction his struggles gave the being that had imprisoned him that he went against his own nature, becoming passive and giving up all attempts to fight free of its hold on him.

His determination to not give it what it wanted clearly annoyed it, as it complained bitterly. “Why do you stop? That is not the way of the warrior?”

“I prefer to know more about my opponent before I engage with them,” Khan responded.

“Ah,” the beings voice became thoughtful. “You wish to assess your opponent’s weaknesses so that you might exploit them.”

“Correct.”

“Then you must prepare to be disappointed, for I possess no weakness,” the being gloated.

“Impossible.”

“And yet it is so,” came the taunting reply.

Realising he wasn’t going to get anywhere with this line of questioning, Khan tried another. “Who are you?”

“I am Armus,” it stated proudly.

“And what is Armus?” Khan queried.

“The physical manifestation of evil,” came back the response.

“Impossible.”

“And yet it is so,” Armus parroted back.

Khan could feel his frustration and impatience growing with Armus, and silently prayed that Spock and McCoy were working on a way to extract him.

*

Getting out his communicator Spock attempted to contact those aboard the Vengeance. “Spock to Captain Kirk.”

But there was no response.

While Spock continued in his attempts, McCoy was checking some new data that had appeared on his tri-corder.

“There’s a recently created energy field that appears to be blocking our ability to contact the ship,” he reported.

Spock checked the readings on his own tri-corder. “It wasn’t there before.”

“Which is why I noted that it was newly created,” the doctor replied in obvious irritation.

*

“How did you come to be on this planet?” Khan asked, looking for anything he could use against Armus.

“The race that lived here created me, and then abandoned me,” Armus snarled.

All of a sudden Khan felt overwhelmed by a powerful landslide of hurt, anger and bitter malice that washed over him. He smiled triumphantly to himself. He had found a chink in Armus’ armour. Now all he had to do was find a way to exploit it.

*

“Did you see that?” Bones asked, indicating the readings on the tri-corder.

“Curious,” Spock said before noting. “Something was strong enough to weaken the force field briefly,” he paused, deep in thought. Looking over at the being that had captured Khan, he turned back to the doctor and speculated. “Is it possible that Khan and this being are communicating?”

“And if they are,” McCoy replied. “Whatever they’re discussing is annoying the creature enough that its energies are becoming compromised.”

“Indeed,” Spock agreed, before taking a cautious step towards the being. “Khan, if you can hear me. Whatever you’re doing, keep doing it.”

*

“Whatever you’re doing, keep doing it.”

Khan felt immense relief at the words. Clearly this conversation with Armus was showing some sign to Spock and McCoy. He may yet get out of this after all.

Taking a deep breath he ploughed on. Armus had still not given him an answer to his last question, so he pressed on. “Come on Armus, why did they create you only to abandon you? And who are they?”

“Who they are no longer matters, they are long gone,” Armus responded petulantly. “But now thanks to you I will finally get my revenge. The only way you can escape my clutches is if you take me with you on your ship. Then I can track those that abandoned me.”

‘At last!’ Khan thought to himself, as a means to extricate him presented itself. ”What did they do to you to earn such wrath?” he queried innocently.

Armus erupted, roaring in anguish and unrestrained rage and fury.

“They created me as a means of expunging all the evil that lay within them. But in removing the evil they needed to place the evil somewhere, so they created me. Now pure of thought they no longer wished to be reminded of the evil they once possessed so they left, leaving me behind...abandoned.”

Khan could feel Armus’ hold on him weakening, caught up in his memories. And so he made his move, using every inch of his strength he fought his way out of his living prison.

As soon as he began to emerge from the black mass, Spock and McCoy were there to pull him free.

Once Khan was safely clear Spock contacted the Vengeance. “Three for immediate beam out.”

***

VENGEANCE – KHAN & MOLLY’S QUARTERS

When he entered his quarters he was met by the welcome sight of Molly.

“Oh my!” she exclaimed as she took in the sight of him.

Khan looked down at himself and grimaced.

“I think you need a shower,” Molly suggested.

Khan immediately brightened at the prospect.

“Yes I believe we do,” he growled.

“Wha..?” Molly began before giving a squeal of delight as Khan scooped her up in his arms and then headed for the bathroom.

*

Their coupling was brief, but frenzied.

They were on the floor of the shower, Molly on all fours as Khan’s hips pumped wildly, slamming into her cunt again and again from behind.

Although Khan set a punishing pace, his savagery was tempered by tenderness, totally at odds with the aggressiveness displayed. But he was always careful to ensure her comfort, never forgetting his enhanced strength.

Not that Molly found reason for complaint. She was the grateful recipient of his passion. 

In minutes the shower stall was filled with their cries of release.

*

After the shower Khan was preparing to shave, when he glanced in the mirror, and paused.

***

IO FACILITY – CMDR J. R. HARRISON’S QUARTERS - 2258.25

Five days after he woke up Commander John Harrison was released from the Medical Bay. The five days since had been spent trying to make sense of all that he saw and heard around him.

Admiral Marcus was adamant that the best way to recover from the events on QoNo’s was for him to get back to work.

“We really need your expertise John,” the Admiral had pleaded. “Things have stalled during your incapacitation, and we’re in danger of falling behind schedule.”

*

John Harrison was in the process of raising an old style razor to begin shaving, when he froze.

For a brief moment the face looking back at him in the mirror had not been his own And yet the features reflected back at him felt familiar, the face had a regal and noble bearing, the skin darker than his own with hair long enough to be pulled back in a ponytail. In many ways that face felt more recognisable, and right than the one currently looking back at him.

John shook his head, trying to clear it, convinced his eyes were playing tricks on him.

But as he left his quarters, a nagging feeling that something wasn’t right refused to leave him.

***

VENGEANCE – KHAN & MOLLY’S QUARTERS

As the memory faded Khan contemplated the being they had encountered. There were many similarities between himself and Armus.

Both had been created to serve a particular purpose.

They had both been feared by their creators, which had led to their being isolated or abandoned.

These actions had led to feelings of resentment, and a need to strike back at those they felt had betrayed them. In his own case that had led to he and the others like him taking control of Earth that had then led to war, and his exile upon the SS Botany Bay.

And that had ultimately led him here, to the 23rd Century.

Considering all that he had gone through since being awoken, he was thankful for the love and friendship of those on this vessel.

If it wasn’t for them there would have been every chance that he would have ended up with a heart as black as Armus’.

***

**Notes for the Chapter:**

> Good on you if you spotted I’ve used the planet and alien life form from the Star Trek Next Generation episode, Skin of Evil.

**Author's Note:**

> I was originally going to post this at the end of the week. But I kept on editing and rewriting it that I thought the best way to stop would be to just post the damn thing and accept any criticisms with good grace.
> 
> This will be by far the most ambitious story I have taken on so far. As the moment it is still very much in the planning stages. There will (hopefully) be lots of interesting twists and turns along the way. This will include the telling of the whole John Harrison/Section 31 storyline, by expanding on ideas that have already been alluded to in official Star Trek: Into Darkness film, novelisation and graphic novels etc.
> 
> Anyway, I hope you all enjoy this Khanolly story, and please, as always your comments and kudos are greatly appreciated and most welcome.


End file.
